Number Of Molecular Operational Taxonomic Units Research Articles

Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae).

Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M. angusta and M. mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margattea deltodonta J-J He & Z-Q Wang, sp. nov., Margattea cuspidata J-J He & Z-Q Wang, sp. nov., Margattea caudata J-J He & Z-Q Wang, sp. nov., Margattea paratransversa J-J He & Z-Q Wang, sp. nov., Margattea disparilis J-J He & Z-Q Wang, sp. nov., Margattea transversa J-J He & Z-Q Wang, sp. nov., and Margattea bicruris J-J He & Z-Q Wang, sp. nov.

EDNA in a bottleneck: Obstacles to fish metabarcoding studies in megadiverse freshwater systems

AbstractThe current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long‐term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 258 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance‐based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 51.55% success rate in species recovery (133/258), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α‐diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β‐diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi‐marker metabarcoding approaches and tailor‐made (i.e., order‐specific) taxonomic delimitation thresholds.

Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae

AbstractAimTo quantify taxon diversity, biogeographic distributions and patterns of community assembly in xeniid octocorals using molecular operational taxonomic units (MOTUs).LocationRed Sea, Indian and western Pacific Oceans.TaxonXeniidae, a family of reef‐dwelling octocorals (Anthozoa, Octocorallia).MethodsXeniids collected at 13 locations were sequenced at three barcode loci, and assigned to MOTUs defined by minimum genetic distance thresholds. Taxon richness (number of MOTUs) and endemicity (per cent of MOTUs found at a single location) were quantified. Patterns of β‐diversity (species turnover) and phylogenetic β‐diversity (lineage turnover) among geographical regions were visualized using hierarchical clustering, non‐metric multidimensional scaling (NMDS) plots and distance‐decay relationships. Community assembly was investigated by comparing the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) separating species in each assemblage to values generated for null communities.ResultsA genetic distance threshold of 0.3% discriminated 67 MOTUs, with taxon richness ranging from 2–18 MOTUs per site. Out of the 67 MOTUs, 48 (72%) were found at only a single location, and only two spanned both the western Indian and Pacific Oceans. Species turnover among sites was high, but phylogenetic β‐diversity was lower than β‐diversity and differed significantly from null models of community assembly at only two sites. β‐diversity and phylogenetic β‐diversity both increased significantly with geographic distance, and sites clustered into three distinct biogeographic regions (Red Sea and western Indian Ocean; Western Australia; western Pacific Ocean and Great Barrier Reef, Australia). All five major clades of xeniids were represented in each region.Main conclusionsA genetic approach to biodiversity estimation suggests that most xeniid taxa are regional endemics whose geographic distribution is likely governed by dispersal limitation. This conclusion contrasts with published records of certain morphospecies occurrences, which imply that they have broad geographic ranges. So far, the distribution of xeniid biodiversity mirrors that of scleractinian corals, with species richness highest in the Coral Triangle, but endemicity peaking in peripheral areas.

A metagenetic approach for revealing community structure of marine planktonic copepods.

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.

DNA Barcodes for Species Identification in the Hyperdiverse Ant GenusPheidole(Formicidae: Myrmicinae)

DNA sequencing is increasingly being used to assist in species identification in order to overcome taxonomic impediment. However, few studies attempt to compare the results of these molecular studies with a more traditional species delineation approach based on morphological characters. Mitochondrial DNA Cytochrome oxidase subunit 1 (CO1) gene was sequenced, measuring 636 base pairs, from 47 ants of the genus Pheidole (Formicidae: Myrmicinae) collected in the Brazilian Atlantic Forest to test whether the morphology-based assignment of individuals into species is supported by DNA-based species delimitation. Twenty morphospecies were identified, whereas the barcoding analysis identified 19 Molecular Operational Taxonomic Units (MOTUs). Fifteen out of the 19 DNA-based clusters allocated, using sequence divergence thresholds of 2% and 3%, matched with morphospecies. Both thresholds yielded the same number of MOTUs. Only one MOTU was successfully identified to species level using the CO1 sequences of Pheidole species already in the Genbank. The average pairwise sequence divergence for all 47 sequences was 19%, ranging between 0–25%. In some cases, however, morphology and molecular based methods differed in their assignment of individuals to morphospecies or MOTUs. The occurrence of distinct mitochondrial lineages within morphological species highlights groups for further detailed genetic and morphological studies, and therefore a pluralistic approach using several methods to understand the taxonomy of difficult lineages is advocated.